Public bug reported:

Hello guys :)
mplayer seems to always swap channels when trying to play 5.1 faad mkv file. 
For example, left speaker plays content intended to be played through the 
center speaker. I had to craft a script which redirects all channels to correct 
speakers. totem handles the playback correctly.
mplayer: 1.0rc2-4.3.3
totem: 2.26.1

the script:
#!/bin/bash
# somehow mplayer has AAC/FAAD channels switched
# the codec outputs channels in the following ordering: CE,FL,FR,RL,RR,LFE, but 
pulseaudio expects the following ordering: FL,FR,RL,RR,CE,LFE.
# we thus need to map first channel to fifth speaker, etc.
MAP="6"
# First channel: map to fifth
MAP=$MAP":0:0:0:0:1:0"
# Second channel: map to first
MAP=$MAP":1:0:0:0:0:0"
# Third channel: map to second
MAP=$MAP":0:1:0:0:0:0"
# Fourth channel: map to third
MAP=$MAP":0:0:1:0:0:0"
# Fifth channel: map to fourth
MAP=$MAP":0:0:0:1:0:0"
# Sixth channel: map to sixth
MAP=$MAP":0:0:0:0:0:1"
mplayer -af pan=$MAP "$@"


Recently I found a patch to mplayer which perhaps fixes the bug: 
http://archives.free.net.ph/message/20090809.234723.559a036b.en.html
The link contains tons of useful information.

** Affects: mplayer (Ubuntu)
     Importance: Undecided
         Status: New

** Description changed:

  Hello guys :)
- mplayer seems to always swap channels when trying to play 5.1 faad mkv file. 
For example. right speaker plays content intended to be played through the 
center speaker. I had to craft a script which redirects all channels to correct 
speakers. totem handles the playback correctly.
+ mplayer seems to always swap channels when trying to play 5.1 faad mkv file. 
For example, left speaker plays content intended to be played through the 
center speaker. I had to craft a script which redirects all channels to correct 
speakers. totem handles the playback correctly.
  mplayer: 1.0rc2-4.3.3
  totem: 2.26.1
  
  the script:
  #!/bin/bash
  # somehow mplayer has AAC/FAAD channels switched
  # the codec outputs channels in the following ordering: CE,FL,FR,RL,RR,LFE, 
but pulseaudio expects the following ordering: FL,FR,RL,RR,CE,LFE.
  # we thus need to map first channel to fifth speaker, etc.
  MAP="6"
  # First channel: map to fifth
  MAP=$MAP":0:0:0:0:1:0"
  # Second channel: map to first
  MAP=$MAP":1:0:0:0:0:0"
  # Third channel: map to second
  MAP=$MAP":0:1:0:0:0:0"
  # Fourth channel: map to third
  MAP=$MAP":0:0:1:0:0:0"
  # Fifth channel: map to fourth
  MAP=$MAP":0:0:0:1:0:0"
  # Sixth channel: map to sixth
  MAP=$MAP":0:0:0:0:0:1"
  mplayer -af pan=$MAP "$@"
  
  
  Recently I found a patch to mplayer which perhaps fixes the bug: 
http://archives.free.net.ph/message/20090809.234723.559a036b.en.html
  The link contains tons of useful information.

-- 
incorrect channel ordering for 5.1 in mplayer
https://bugs.launchpad.net/bugs/421009
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